Eliceiri Lab

ImageJ is an open source image processing
package popular in microscopy, medical imaging, plant sciences and other
areas of scientific imaging. ImageJ's greatest strength is its flexible
plugin mechanism, allowing scientists to extend its functionality by
writing plugins and scripts to perform custom processing. Despite the
flexibility and modularity of ImageJ, it lacks an image informatics
infrastructure. Fixing this deficiency is the goal of this project. Both
OMERO and ImageJ are designed to work with the same sorts of image data.
The difference is that OMERO provides a robust server infrastructure for
centralized storage and analysis of life sciences images, while ImageJ
is a standalone tool for use on desktop workstations. However, both
support life sciences data via the Bio-Formats library, and both handle
datasets of up to five dimensions (X, Y, Z, time and channel). Further,
increasingly popular multidimensional modalities such as spectral and
lifetime imaging require image analysis software to support dimensions
beyond these five. As such, both OMERO and ImageJ are now actively
developing support for additional dimensions of image analysis.

LOCI's ImageJ-OMERO project
seeks to extend ImageJ for easier interoperability with OMERO. OMERO
should be capable of executing ImageJ plugins for multidimensional image
processing within the OMERO server, using ImageJ as a library. And ImageJ
should be able to access image data from OMERO data, process it locally,
and then upload the results back to the OMERO server. OMERO benefits from
ImageJ's easy extensibility and large collection of existing scripts and
plugins, and ImageJ benefits from OMERO's centralized storage and
unified metadata model. With this synergy, this is clearly a great
opportunity to bring the full power of community-based image processing
to bench scientists.

Kevin Eliceiri is Director of the Laboratory for
Optical and Computational Instrumentation (LOCI) at the University of
Wisconsin-Madison. LOCI is an NSF and NIH-funded instrumentation group
with the mission of developing advanced optical and computational
techniques for imaging and experimentally manipulating living specimens.
Kevin leads these efforts and is working on utilizing the OME system as
a visualization framework for multidimensional biological image data.

Curtis Rueden is a software architect at LOCI at the
University of Wisconsin-Madison. Together with Kevin, Curtis directs
LOCI's software efforts as a whole. Curtis is also the maintainer of
the SciJava software stack including
ImageJ, Fiji,
SCIFIO and
SciJava Common.
Curtis designed the original Bio-Formats library API, and
spearheaded the original OME-TIFF file format.
Before joining LOCI, Curtis was part of UW-Madison's
SSEC Visualization Project
as a developer of the
VisAD
Java component library.

Alison Walter is a student programmer at LOCI.
She works on several projects, including
ImageJ Ops and
ImageJ-OMERO.

Mark Hiner was a software developer at LOCI from
September 2010 - June 2016. Mark worked on
ImageJ and SCIFIO.

Johannes Schindelin was a senior software
developer at LOCI from September 2011 - September 2014. Johannes
focused on developing software tools to help biologists analyze
microscopy data. These days, Johannes works for Microsoft on the
Git for Windows project.

Kristin Briney was a Library Sciences student at LOCI,
working to streamline the acquisition of experimental data beyond the
biological image. She helped drive LOCI metadata efforts,
and corresponding improvements to the OME data model.

Melissa Linkert — Melissa has moved to work on Bio-Formats for
Glencoe Software.